SAW User Manual V8.0
  • Overview
  • Getting Started
    • Introduction
    • Glossary
  • Download Center
  • Analysis
    • Inputs
      • Chip mask
      • FASTQs
      • Images
    • Pipelines
      • SAW commands
      • count
        • Stereo-seq T FF
        • Stereo-seq N FFPE
    • Outputs
      • count outputs
      • realign outputs
      • HTML report
      • BAM
      • Matrices
      • Images
      • Analysis
  • Tutorials
    • Preparation of reference
    • Stereo-seq FF
    • Stereo-seq FFPE
    • With manually processed files
    • Secondary analysis
    • Format conversion
  • Algorithms
    • Read processing algorithms
    • Image processing algorithms
  • Advanced
    • Analysis with GPU
    • Expression matrix format
    • Image-related record format
  • Release Notes
  • SUPPORT PAGES
    • Datasets
    • Troubleshooting
    • Software and Kit Compatibility
    • Q & A
    • StereoMap
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  • SAW
  • What is SAW?
  • Analysis
  • Tutorials

Last updated 8 months ago

SAW

What is SAW?

Stereo-seq Analysis Workflow (SAW) software suite is a set of pipelines bundled to map sequenced reads to their spatial location on the tissue section, quantify spatial feature expression, and visually present spatial expression distribution. SAW processes the data from the Stereo-seq sequencing platform, combined with microscope images, to generate spatial feature expression matrices. Analysts can use the output files as a starting point to perform downstream analysis.

Analysis

Tutorials

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Download SAW

Get Started With SAW

Download Datasets

Inputs

Learn about preparatory input files to run SAW

Pipelines

Learn about how to run SAW piprlines

Outputs

Learn about output files generated from SAW

SAW for Stereo-seq FF

Learn how to perform SAW count on fresh frozen (FF) samples

SAW for Stereo-seq FFPE

Learn how to perform SAW count on formalin-fixed paraffin-embedded (FFPE) samples

With manually processed files

Learn how to handle with manually processed images from StereoMap